Alaska Sustainable Salmon Fund Statement of Work I. Project Title: Yentna Sonar Error Estimation II. Project Number: PCSRF Objective: RM&E III. Principal Investigator: Suzanne Maxwell, Fishery Biologist ADF&G, Commercial Fisheries Division 43961 K-Beach Road, Suite B Soldotna, AK 99669 Phone: (907) 260-2914 Email: suzanne.maxwell@alaska.gov IV. Project Period: 7/1/09-3/15/13 V. Project Description 1. Introduction The Yentna Sonar Error Estimation project is designed to determine the error inherent in estimates of sockeye salmon abundance determined from a long-standing sonar project on the Yentna River. The original sonar project has provided daily abundance estimates of sockeye salmon migrating upriver to commercial fishery managers and user groups for the management of commercial fisheries in Upper Cook Inlet. The estimates of migrating fish were generated from a Bendix sonar counter and apportioned to salmon species using catch information from fish wheels. In recent years, these abundance estimates have come into question. A combination of upstream weir counts, counts from a more modern sonar system (a dual-frequency identification sonar (DIDSON)), and mark-recapture abundance estimates all suggest the sonar and fish wheel generated estimates are biased low. Preliminary results from a side-by-side DIDSON and Bendix comparison study showed the DIDSON estimates to be almost double the Bendix estimates. Mark recapture abundance estimates suggest that the estimates based on DIDSON may also be biased low. The use of the DIDSON for the purpose of counting migrating sockeye salmon in rivers has been examined in clear rivers, and estimates have been shown to be both accurate and precise, but the Yentna River presents challenges not faced in a clear river study. The river is wider, highly turbid, and the river bottom topography is not ideal for sonar sampling. However, the greatest challenge stems from the species apportionment program, which uses fish wheel catches to apportion the sonar estimates to species. All five species of Pacific salmon migrate past the Yentna River site and share similar run timing. The apportionment procedure may account for the largest source of error. According to Meehan (1961), pink salmon are four times more likely to be captured in fish wheels as sockeye and chum salmon, which violates the primary assumption of the apportionment program, that each passing fish, regardless of length or species, has the same probability of capture in the fish wheel. Yentna Sonar Error Estimation page 1 of 11 1/30/2013
To address these issues, potential site-specific error sources in the Yentna River sonar project have been identified and include: 1) the sampling design, 2) observer counting errors, 3) truncating the field season, 4) fish migrating outside the sonar beam, 5) reduced detection of fish within the sonar beam, and 6) uneven capture probabilities from the fish wheel. The DIDSON s sampling design (1) is similar to that employed at tower sites to count sockeye salmon, so the uncertainty has been examined and can be estimated. Of the identified potential error sources, this is the only one that has been addressed. 2. Project Summary This project will examine five error sources of estimating salmon abundance on the Yentna River using DIDSON and evaluate whether the new methods provide a more accurate sockeye salmon abundance estimate by comparing old and new estimates with aggregate upstream weir counts. The following error sources will be investigated: observer counting errors, truncation of the field season, fish migrating outside the sonar beam, reduced detection of fish within the sonar beam, and uneven capture probability in the fish wheel. 3. AKSSF Objective Central: 2A-3 VI. Objectives 1. Project Objectives 1. Estimate the effect of multiple observers on the accuracy and precision of the sonar estimates. 2. Determine whether the timing of the field season has biased the salmon escapement estimates. 3. Estimate the number of fish migrating outside of the sonar beam. 4. Determine whether pink salmon can be accurately extracted from the mix of salmon species. 5. Estimate the proportion of pink salmon within the range of the fish wheel and the total proportion using DIDSON range and length data, and compare the first estimate with the actual fish wheel catch, and the second estimate with the fish wheel selectivity-corrected apportionment provided through the AKSSF project Yentna Fish Wheel Selectivity. 2. Justification Unknown errors that produce lowered salmon abundance estimates have the potential to close fisheries, while erring on the high side may adversely affect future salmon runs. Each of the objectives listed above brings the estimated abundance closer to the true population. Objective 1: Estimating the precision between different observers is necessary because multiple observers are employed to manually count the DIDSON images. In recent years a much higher than usual turn-over rate among employees has increased the likelihood that the counts will vary as the newcomers gain experience. Yentna Sonar Error Estimation page 2 of 11 1/30/2013
Objective 2: A start date for the sonar project s field operations was selected based on a balancing act between the known run timing of sockeye salmon, commercial fishing schedules, and budgetary concerns. The end-of-sampling date is based on a combination of the cessation of the commercial fishery that targets Yentna River sockeye salmon stocks, and a comparison of the daily sockeye salmon count to the total count. Truncating the sampling on either end has the potential to bias the escapement estimates low. Objective 3: Measuring the effective sampling volume of the sonar beam and estimating the numbers of fish outside this volume is important because the Yentna River is wider and deeper than the dimensions of the sonar beams, with less than 25% of the river width ensonified and incomplete vertical coverage. Objective 4: An assumption of the apportionment method is that all species have equal probability of capture in the fish wheels. If Meehan s findings hold true at the Yentna River site, pink salmon may have a greater opportunity for capture, resulting in lowered sockeye salmon estimates. Constructing a fish length distribution by range will make it possible to determine whether there are significant differences in the lengths of offshore fish. Objective 5: Length measures from DIDSON images have been tested using the low frequency DIDSON and a high resolution lens, but no studies have been done with the more accurate high frequency DIDSON coupled to the same high resolution lens. This project will also test the DIDSON s measurement accuracy using stationary targets in a controlled environment. If the system proves accurate enough, the DIDSON-based length measures will be used at the Yentna River to extract pink salmon from the remaining species. Accurately extracting the pink salmon from the remaining mix of species will greatly improve the accuracy of the sockeye salmon estimates. 3. Project Outcomes The primary anticipated outcome is a more accurate and defensible sockeye salmon abundance estimate for the Yentna River. The criteria used to evaluate the success of this project will include: 1) the establishment of an in-season sonar fish-counting program capable of counting 95% of the migrating fish population, 2) the ability to transfer this methodology to other rivers, and 3) the ability to instill a higher level of confidence in the Yentna River estimates. 4. Methods/Modeling Objective 1: All new project staff will be trained to monitor the DIDSON operations, report problems that arise to the project crew leader, and count fish images from the DIDSON files. Training procedures will be reviewed for returning staff. Each sonar operator, or observer, will be given 30 sample images to count after the training procedures are completed. High, medium, and low passage sample files will be randomly selected from previous years data grouped by passage rate. The accuracy of each count will be assessed by comparing the counts from each observer to counts from a highly trained sonar operator. Observers will be asked to count a second set of Yentna Sonar Error Estimation page 3 of 11 1/30/2013
sample files toward the end of the field season to determine the effects of experience on the sonar counts. The relative precision from all observers will be calculated. Objective 2: To determine whether the timing of the field season has biased the escapement estimates, the effect of the start and end dates on each year s total count will be examined. Traditionally, the criteria used to decide when to stop counting fish at the Yentna River sonar project is the 1% rule. Field operations continue until the daily count drops below 1% of the field season s cumulative count for three days following the final commercial fishing period within that district. The rule for the field season start date is less concrete. The first four years of field operations began on July 1 except for 1986 when the field season was started two days earlier. After four years, a start date of July 7 was chosen for all remaining years. For this objective, the 1% rule will be applied to determine which years were truncated. To predict the total run during years when the 1% rule was not met on either the front or end of the run, this project will 1) plot the daily counts from each year, 2) line up the peaks to remove differences in run timing, 3) average each curve which met the 1% rule for the start date, 4) average each curve which met the 1% rule for the end date, 5) determine the average of the daily count divided by the season s total count for the first and last weeks of each run, 6) use these averages to expand the data for years the 1% rule was not met, and 7) compare the actual totals and newly estimated totals to determine the effect of the truncated field seasons on the annual estimates of abundance. Objective 3: To estimate fish migrating outside of the sonar beam, the first task will be to determine the effective sampling volume of the beam. A salmon-size target will be used to measure the effective limits of the beam by lowering the target to the river bottom and slowly raising it to the surface at successive range intervals until the target is no longer detectable. Once the sampling region is determined, the numbers of fish traveling outside of this region will be assessed. The numbers of fish migrating offshore of the effective sampling region will be determined through two methods, transecting the mid-river region using a mobile DIDSON and deploying a long-range DIDSON offshore of the nearshore DIDSON. A cross-river fish distribution constructed from the data will be used to determine the range interval in which 99% of salmon migrate. As part of this effort, Aquacoustics Inc. will be contracted to conduct a bathymetry survey in the region of the sonar and fish wheel to identify likely fish migration channels. The numbers of fish migrating above the effective sampling volume of the beam will be determined by deploying DIDSONs along each side of the river with the lens positioned vertically. In this configuration, the DIDSON beam is roughly twice the depth of the sampling beam, and an accurate determination of where fish are vertically in the water column can be determined. From this data, a vertical distribution of fish will be constructed. The effective volume of the sampling DIDSON will be overlaid on this distribution, and the percentage of fish above this beam determined. To accomplish this objective, Bill Hanot of Sound Metrics Corporation will develop the software needed to efficiently process the vertical data. He will also perform field testing for software previously Yentna Sonar Error Estimation page 4 of 11 1/30/2013
developed that uses a timed program to automate the DIDSON between a vertical and horizontal configuration. Objective 4: The accuracy and precision of image length measurements obtained using a standard DIDSON with a high resolution lens will be assessed by measuring a series of known targets in a controlled environment. Sound Metrics Corp., the DIDSON manufacturers, developed a higher resolution lens that narrows the field of view, increasing the cross-beam resolution to 2.6 cm at 10 m. A series of 30 targets will be measured from DIDSON images, and the measurements compared to actual target lengths. From this comparison, the accuracy of each target s image length will be determined and whether a range-dependent bias is detectable within these measures will be examined. A high resolution DIDSON will be deployed near each fish wheel at the Yentna River to measure fish lengths of migrating salmon. A daily random sample of fish images within the range of the fish wheel will be measured. Although length frequency curves for the various salmon species at the Yentna River have been constructed in the distant past, recent measurements at this site include only sockeye salmon. As part of this study, the fish wheel program at the Yentna River will be expanded to include measurements from all salmon species. Length frequency curves will be constructed from the actual fish measurements and a mixture model approach will be used to determine whether pink salmon can be accurately extracted from the species mix. The same mixture model will be applied to DIDSON length measurements to determine whether fish can be divided into two groups, pink salmon and a mixture of sockeye, coho, and chum salmon. Objective 5: Using the dataset of high resolution fish images collected for the previous objective, a daily sample of fish images will be measured and a length distribution by range will be constructed. The size of this sample will depend on whether the fish sizing tools have been automated. The fish length distribution will be divided into two groups, nearshore fish within the range of the fish wheel and offshore fish migrating beyond this range. Using the mixture model, pink salmon will be extracted from the remaining fish. From the nearshore and offshore sets of these three fish groupings, this project will determine 1) the percentage of fish traveling beyond the range of the fish wheel, 2) whether offshore fish are significantly different in size than the nearshore fish, and 3) whether there is a correlation between fish length and distance from shore. The sonar-apportioned fish will be compared with the proportions derived from the fish wheel. For the first comparison, fish within the range of the fish wheel will be compared. For the second comparison, all fish measured by the sonar with selectivity-corrected fish wheel proportions will be compared. The selectivity-corrected fish wheel proportions will be contributed from AKSSF project Yentna Fish Wheel Selectivity. Standard and multiple regression techniques will be used for each comparison. Other variables that will be included in the multiple regressions include water level and fish density derived from the sonar counts. As the water level increases or decreases, and current velocity changes, fish may be forced closer to shore at higher rates and may spread further from shore at lower current velocities. Fish density is a second factor that will be considered. It has been observed that as sockeye salmon increase in density, they move closer to Yentna Sonar Error Estimation page 5 of 11 1/30/2013
shore. When the density of any one species increases, this may affect the other species. The overall count from the unapportioned sonar will be used to estimate the fish density. VII. Results/Deliverable Products The results of this project will be summarized in semiannual and annual reports, a final, comprehensive report, a peer-reviewed journal article, and oral presentations at both local and nation-wide forums. The dates for each of these deliverables are: October 31, 2010, 2011, 2012, and 2013 Annual reports summarizing the project s progress will be completed. February 1, 2010, 2011, 2012, and 2013 Semiannual reports will be finalized summarizing the project s progress. March 1, 2013 An article presenting the results of the fish length studies will be submitted to a peer-reviewed journal. March 15, 2013 A comprehensive plan to improve the accuracy of the sonar estimates that can be applied to any riverine system will be produced. March 15, 2013 The final report will be completed. Jan - March 15, 2013 The final results from this project will be presented at local and nation-wide American Fisheries Meetings and the other acoustical meetings where appropriate. Any detailed formal project report for publication will include the following language: This [report/video/website] was prepared by [recipient/author name] under award #NAO8NMF4380597 from the National Oceanic and Atmospheric Administration, U.S. Department of Commerce, administered by the Alaska Department of Fish and Game. The statements, findings, conclusions, and recommendations are those of the author(s) and do not necessarily reflect the views of the National Oceanic and Atmospheric Administration, the U.S. Department of Commerce, or the Alaska Department of Fish and Game. PI will submit semiannual, PCSRF performance metrics, and project completion reports according to the AKSSF schedule, as well as copies of any other report/product/ deliverable produced with this funding. VIII. Benefits to Salmon/Salmon Fisheries/Salmon Fishermen/Communities A more accurate assessment of the Yentna River sockeye salmon stocks will benefit user groups, fishery managers, fish processors, and agencies interested in the health and status of Upper Cook Inlet salmon. Minimizing this uncertainty will allow fishery managers to better utilize this valuable resource. If the existing estimates are higher then the true migrating salmon population, there is potential to over harvest fish and put the salmon stocks at risk; if lower, harvest opportunity may be lost. IX. Project Milestones and Timelines Date FY Event July 7-Aug 15, 2009 FY10 Data collection - 1 st season, bathymetry work completed (Aquacoustics); software development for the vertical data processing begun (Bill Hanot). Yentna Sonar Error Estimation page 6 of 11 1/30/2013
July 7-Aug 15, 2010 Feb 2011 March 15, 2011 July 7-Aug 15, 2011 July 7-Aug 15, 2012 March 15, 2013 FY11 FY11 FY11 FY12 FY13 FY13 Data collection - 2 nd season; data collected for objectives 1 and 3-5. Preliminary results presented at Upper Cook Inlet fisheries board meeting. Software development finalized and testing completed. Data collection - 3 rd season, data collected for objectives 1 and 3-5. Data collection - Final season, data collected to satisfy objectives 1 and 3-5. Project Completion report and comprehensive plan completed; peer-review article submitted. Spring 2013 FY13 Data presented at appropriate scientific forums. Prior to commencement of project activity, the PI will obtain ADF&G employee collection, Fish Resource, Fish Transport, and/or other required permits, as appropriate. All invoices will be submitted for payment in approvable form within 30 days of project end date. X. Partners Cook Inlet Aquaculture Association will operate upriver weirs to provide a measure of comparison for the success of this project. Debby Burwen (ADF&G, Sport Fish Division) is developing an automated DIDSON tool to measure image lengths currently being developed through AKSSF project 45851 and Carl Pfisterer (ADF&G, Commercial Fisheries Division) is developing a more efficient echogram program to process DIDSON files. XI. Project Budget FY10 FY11 FY12 FY13 Total 100 Personnel $0 $57,171 $56,883 $56,883 $170,937 200 Travel $0 $0 $0 $0 $0 300 Contractual $16,470 $10,530 $4,000 $4,000 $35,000 400 Supplies $22,900 $1,800 $1,000 $1,000 $26,700 500 Equipment $386,000 $0 $0 $0 $386,000 Total Direct Costs $425,370 $69,501 $61,883 $61,883 $618,637 ADF&G 3% $18,559 Total $637,196 Yentna Sonar Error Estimation page 7 of 11 1/30/2013
Budget Narrative: Line 100: April Faulkner, designated project leader, and Theodore Hacklin will assist with higher level data processing and crew direction. The technician, unknown at this time, will be hired for the FY11 season. Line 300: Travel to the Yentna site is included in line 300 funds because commercial flights are not available to this region and chartering is necessary. Expenses will be spared whenever possible by sharing flights with the existing project. Aquacoustics Inc. will be contracted to do a comprehensive bathymetric analyses of the sonar and fish wheel sites needed for Objective 3. Don Degan is the contact for Aquacoustics, Inc. P.O. Box 1473, Sterling, Alaska 99672; phone: (907) 260-6341. Sound Metrics will be contracted to write the needed software to process the vertical data for Objective 3. Bill Hanot is the software developer at Sound Metrics 15029 Bothell Way, Suite 100, Lake Forest Park, WA 98155; phone: (206) 364-1441. These and remaining items are detailed in the table below. FY13 costs are identical to FY12 and are included in the totals below. Yentna Sonar Error Estimation page 8 of 11 1/30/2013
Budget Detail: FY10 FY11 FY12 (FY13 is the same) Description days or no. unit rate cost days or no. unit rate cost days or no. unit rate cost Personnel (Line 100) Technician II 0 $189 $0 57 $189 $10,773 56 $189 $10,584 Theodore Hacklin 0 $363 $0 90 $363 $32,670 89 $363 $32,307 April Faulkner 0 $264 $0 52 $264 $13,728 53 $264 $13,992 Travel (Line 200) Contractual (Line 300) Hi Adventure - contract flights to Yentna. Each flight is a oneway. 4 $1,000 $4,000 4 $1,000 $4,000 4 1000 $4,000 Aquacoustics - bathymetry (see above narrative) 6.5 $913.85 $5,940 Sound Metrics - DIDSON software development (see above narrative) 5 $1,306 $6,530 5 $1,306 $6,530 Supplies (Line 400) generators and batteries varied $6,600 electronic and power supplies varied $3,500 varied $1,000 varied $1,000 mounts 2 $400 $800 target supplies and fabrication 1 $800 $800 computers to operate DIDSONs 4 $3,000 $12,000 Equipment (Line 500) DIDSON & cables (3 std and 1 LR) 4 $78,000 $312,000 high res. lens 2 $7,000 $14,000 automated rotators 4 $15,000 $60,000 Annual Totals $425,370 $69,501 $61,883 Total All Years: $618,637 Needed Match Funds $204,150 $140,372 $22,935 $20,421 Budget adjustments between line items are allowed for amounts equal to or less than 10% of the total award without prior AKSSF approval; any amount above 10% requires prior AKSSF approval. All costs in lines 100-500 must represent actual cash expenditures. All requests for reimbursement shall be adequately documented with both documentation of expense and proof of payment. Examples of expense documentation include copies of invoices, pay stubs, receipts, etc. Documentation of proof of payment includes copies of checks, check numbers, credit card receipts, etc. Yentna Sonar Error Estimation page 9 of 11 1/30/2013
All invoices must be submitted for payment in approvable form within 30 days of project end date. Invoices submitted after that deadline will not be reimbursed. Invoices for expenses incurred after the project end date will not be reimbursed. XII. Match Budget FY10 FY11 FY12 FY13 Total 100 Personnel $80,376 $23,152 $20,520 $20,520 $144,568 200 Travel $0 $0 $0 $0 $0 300 Contractual $54,000 $0 $0 $0 $54,000 400 Supplies $6,000 $0 $0 $0 $6,000 500 Equipment $0 $0 $0 $0 $0 Total Direct Costs: $140,376 $23,152 $20,520 $20,520 $204,568* *Match budget shows more match than is required for this project. Total General Fund match: $204,151 Match Budget Narrative: The match funds are from State of Alaska general funds and cover salaries and equipment needed to run the project. Line 100: Suzanne Maxwell (principal investigator) at a rate of $392/day (65 days in FY10 = $25,480, 19 days in FY11 = $7,448, 17 days in FY12 = $6,664, and 17 days in FY13 = $6,664). Total: $46,256. April Faulkner (project leader) at a rate of $264/day (86 days in FY10 = $22,704, 30 days in FY11 = $7,920, 23 days in FY12 = $6,072, and 23 days in FY13 = $6,072. Total: $42,768. Theodore Hacklin (fishery biologist) at a rate of $7,784 per month, which includes 60 h overtime. During the field season, staff at the Yentna work 7 days/week. One month of his time is included in each fiscal year. In FY10, an additional 39 non-field days are included at a rate of $242/day; 1 month and 39 days total $17,222. Stan Walker (fishery technician) in FY10 only, at a rate of $6,964 for 1 month, which includes 60 h overtime. Kris Dent (fishery technician) in FY10 only, at a rate of $5,976 for 1 month, which includes 60 h overtime. Xinxian Zhang (biometric and editorial support) 5 days in FY10 at a rate of $406/day = $2,030. Line 300: Yentna Sonar Error Estimation page 10 of 11 1/30/2013
Three DIDSONS (two standard and one long-range) @ $12,000/mo for 1.5 months each in FY10 (3 * 1.5 * $12,000 = $54,000). Line 400: Two field computers at $3,000 ea. totaling $6,000. Yentna Sonar Error Estimation page 11 of 11 1/30/2013